Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single cell resolution [scRNA-seq]

Here, we developed a single-cell sequencing method based on combinatorial hybridization to generate a tissue-based transcriptomic landscape of the neotenic and metamorphosed axolotl. We performed gene expression profiling of over 1 million single cells across 19 tissues to construct the first adult axolotl cell landscape. Comparison of single-cell transcriptomes between the tissues of neotenic and metamorphosed axolotls revealed the heterogeneity of non-immune parenchymal cells in different tissues and established their regulatory network. Furthermore, we described dynamic gene expression patterns during limb development in neotenic axolotls. This system-level single-cell analysis of molecular characteristics in neotenic and metamorphosed axolotls, serves as a resource to explore the molecular identity of the axolotl and facilitates better understanding of metamorphosis. Bulk RNA sequencing datasets for seventeen adult neotenic axolotl tissues (brain, bladder, cloaca, eye, fore limb, hind limb, gill, gonad, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail) and fourteen adult metamorphosed axolotl tissues (bladder, brain, cloaca, eye, hind limb, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail). Single cell combinatorial hybridization RNA sequencing datasets for nineteen adult neotenic axolotl tissues (brain, bladder, cloaca, eye, fore limb, hind limb, gill, gonad, pancreas, prostate, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail), sixteen adult metamorphosed axolotl tissues (bladder, brain, cloaca, eye, fore limb, hind limb, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail, gonad).